Impact of DNA ligase 1 and IIIα interactions with APE1 and polβ on the efficiency of base excision repair pathway at the downstream steps

J Biol Chem. 2024 Jun;300(6):107355. doi: 10.1016/j.jbc.2024.107355. Epub 2024 May 7.

Abstract

Base excision repair (BER) requires a tight coordination between the repair enzymes through protein-protein interactions and involves gap filling by DNA polymerase (pol) β and subsequent nick sealing by DNA ligase (LIG) 1 or LIGIIIα at the downstream steps. Apurinic/apyrimidinic-endonuclease 1 (APE1), by its exonuclease activity, proofreads 3' mismatches incorporated by polβ during BER. We previously reported that the interruptions in the functional interplay between polβ and the BER ligases result in faulty repair events. Yet, how the protein interactions of LIG1 and LIGIIIα could affect the repair pathway coordination during nick sealing at the final steps remains unknown. Here, we demonstrate that LIGIIIα interacts more tightly with polβ and APE1 than LIG1, and the N-terminal noncatalytic region of LIG1 as well as the catalytic core and BRCT domain of LIGIIIα mediate interactions with both proteins. Our results demonstrated less efficient nick sealing of polβ nucleotide insertion products in the absence of LIGIIIα zinc-finger domain and LIG1 N-terminal region. Furthermore, we showed a coordination between APE1 and LIG1/LIGIIIα during the removal of 3' mismatches from the nick repair intermediate on which both BER ligases can seal noncanonical ends or gap repair intermediate leading to products of single deletion mutagenesis. Overall results demonstrate the importance of functional coordination from gap filling by polβ coupled to nick sealing by LIG1/LIGIIIα in the presence of proofreading by APE1, which is mainly governed by protein-protein interactions and protein-DNA intermediate communications, to maintain repair efficiency at the downstream steps of the BER pathway.

Keywords: AP-endonuclease 1; DNA ligase 1; DNA ligase IIIα; DNA polymerase β; DNA repair; base excision repair; genome stability; protein-DNA binding; protein–protein interaction.

MeSH terms

  • DNA Ligase ATP* / chemistry
  • DNA Ligase ATP* / genetics
  • DNA Ligase ATP* / metabolism
  • DNA Polymerase beta* / chemistry
  • DNA Polymerase beta* / metabolism
  • DNA Repair*
  • DNA-(Apurinic or Apyrimidinic Site) Lyase* / chemistry
  • DNA-(Apurinic or Apyrimidinic Site) Lyase* / genetics
  • DNA-(Apurinic or Apyrimidinic Site) Lyase* / metabolism
  • Excision Repair
  • Poly-ADP-Ribose Binding Proteins
  • Protein Binding

Substances

  • DNA Ligase ATP
  • DNA Polymerase beta
  • DNA-(Apurinic or Apyrimidinic Site) Lyase
  • Poly-ADP-Ribose Binding Proteins